\name{helpList} 
\alias{helpList} 
\docType{package} 
\title{
Functions defined by MIfuns
}
\description{Exhaustive list of functions (etc.) defined by MIfuns.}
\details{
\itemize{
\item \link{\%nested.in\%} test whether a is nested in b
\item \link{\%nests\%} test whether a nests b
\item \link{AUC} calculate the area under the curve for each subject over the time interval for dv using the trapezoidal rule.
\item \link{CLNR} delete files and directories and log what was deleted to a text file in the ProjectDir
\item \link{CheckPositiveMatrix} determine if omega matrix is positive, definite (\code{SimulationFromFile})
\item \link{CheckPositiveVector} determine if omega matrix is positive, definite (\code{SimulationFromFile})
\item \link{ComputePredictiveCheck} compute individual patient parameters for observed data and for each simulated study; compute statistics of individual parameters for each study (beta)
\item \link{CreateParametersForSimulation} generate nsim sets of model parameters for simulation based on the results of a (final) model
\item \link{NONR} run NONMEM and create diagnostic plots
\item \link{Omega.MtoV} convert matrix containing omega estimates into a vector of omega estimates
\item \link{Omega.VtoM} convert vector containing lower block omega estimates into a full matrix of omega estimates
\item \link{Ops.keyed} use concise syntax to join data frames
\item \link{PLOTR} create diagnostic plots for NONMEM runs
\item \link{PlotPredictiveCheck} plot results of \code{\link{ComputePredictiveCheck}}
\item \link{SimulateOmega} generate omega values for simulation
\item \link{Tmax} calculate the time associated with the maximum concentration for each subject
\item \link{Tmin} calculate the time associated with the minimum concentration for each subject
\item \link{TruncateParametersForSimulation} truncate a set of parameters for simulation according to a user-defined set a boundaries
\item \link{[.comment} subset a comment
\item \link{[.flag} subset a flag
\item \link{[.keyed} subset a keyed data frame
\item \link{[.miTemporal} subset a miTemporal object
\item \link{[<-.miTemporal} assign to a miTemporal object
\item \link{[[.comment} select element from a comment
\item \link{[[.flag} select element from a flag
\item \link{[[.miTemporal} select element from a miTemporal object
\item \link{accept} document the acceptance of an R installation
\item \link{acceptance} display the acceptance documentation for an R installation
\item \link{acr} calculate accumulation ratio
\item \link{aggregate.keyed} aggregate a keyed data frame
\item \link{and.keyed} produce inner join of two keyed data frames
\item \link{as.character.comment} convert comment to character
\item \link{as.character.flag} convert flag to character
\item \link{as.character.miTemporal} convert miTemporal to character
\item \link{as.chartime} convert to time (generic, internal)
\item \link{as.chartime.numeric} convert numeric to time
\item \link{as.comment} convert to comment
\item \link{as.comment.comment} convert comment to comment
\item \link{as.comment.default} convert default to comment
\item \link{as.csv.filename} convert to csv.filename
\item \link{as.csv.filename.character} convert character to csv.filename 
\item \link{as.data.frame.comment} convert comment to data frame
\item \link{as.data.frame.flag} convert flag to data frame
\item \link{as.filename} convert to filename
\item \link{as.filename.character} convert character to filename
\item \link{as.flag} convert to flag
\item \link{as.flag.default} convert default to flag
\item \link{as.flag.flag} convert flag to flag
\item \link{as.keyed} convert to keyed
\item \link{as.keyed.data.frame} convert data frame to keyed
\item \link{as.miDate} convert to miDate
\item \link{as.miDate.miDate} convert miDate to miDate
\item \link{as.miDate.character} convert character to miDate
\item \link{as.miDate.dates} convert dates (chron) to miDate
\item \link{as.miDate.miDate} convert miDate to miDate
\item \link{as.miDate.numeric} convert numeric to miDate
\item \link{as.miDateTime} convert to miDateTime
\item \link{as.miDateTime.POSIXct} convert POSIXct to miDateTime
\item \link{as.miDateTime.POSIXlt} convert POSIXlt to miDateTime
\item \link{as.miDateTime.character} convert character to miDateTime
\item \link{as.miDateTime.chron} convert chron to miDateTime
\item \link{as.miDateTime.miDate} convert miDate to miDateTime
\item \link{as.miDateTime.miDateTime} convert miDateTime to miDateTime
\item \link{as.miDateTime.numeric} convert numeric to miDateTime
\item \link{as.miTime} convert to miTime
\item \link{as.miTime.character} convert character to miTime
\item \link{as.miTime.miTime} convert miTime to miTime
\item \link{as.miTime.numeric} convert numeric to miTime
\item \link{as.miTime.times} convert times (chron) to miTime
\item \link{as.moot} convert to moot
\item \link{as.nm} convert to nm (NMTRAN-ready NONMEM data set)
\item \link{as.nm.data.frame} convert data frame to nm
\item \link{as.numeric.chartime} convert chartime to numeric
\item \link{as.rigged} convert to rigged
\item \link{auc} calculate area under the curve
\item \link{aug} add named elements to an object
\item \link{backtrans} backtransform cols in x, returning x
\item \link{badAmt} generic
\item \link{badAmt.nm} AMT is NA where EVID is 1
\item \link{badDv} generic
\item \link{badDv.nm} DV is NA where EVID is 0
\item \link{badII} generic
\item \link{badII.nm} II is greater than 0 where ADDL is NA or 0 (unless SS > 0)
\item \link{bakfor} impute NAs using last observation carried forward after next observation carried backward
\item \link{bin} calculate bin limits for x and place each value in a bin, returning the number of values in each bin
\item \link{bmi} calculate body mass index
\item \link{bsa} calculate body surface area
\item \link{c.comment} combine comment
\item \link{c.flag} combine flag
\item \link{c.miTemporal} combine miTemporal
\item \link{cavg} calculate average concentration
\item \link{check.data} check for missing data, numeric data, ranges, etc.
\item \link{cmax} calculate maximum steady-state concentration
\item \link{cmin} calculate minimum steady-state concentration
\item \link{compileflag} calculate compiler flag for qsub
\item \link{compiler} extract compiler specification from configuration file
\item \link{compute.cwres} compute conditional weighted residuals
\item \link{config} calculate path to configuration file
\item \link{constant} generic
\item \link{constant.default} test whether values of x are contant within an index
\item \link{contains} test a character vector for occurences of a pattern
\item \link{covariatePlots} create diagnostic plots for covariates
\item \link{crcl} calculate creatinine clearance
\item \link{crosses} test whether a crosses b
\item \link{css} calculate steady-state concentration
\item \link{cwresPlots} create conditional weighted residual diagnostic plots
\item \link{dataFormat} combine NONMEM predictions, parameter estimates, and covariates into a standard format (internal)
\item \link{dataSynthesis} build a standard plotting data set for a given NONR run
\item \link{deranged} generic
\item \link{deranged.data.frame} instantiate records implied by range data
\item \link{deranged.keyed} instantiate records implied by range data
\item \link{diagnosticPlots} create standard diagnostic plots
\item \link{distance} generic
\item \link{distance.logical} calculate the position of each element of a logical vector relative to the n-th TRUE element (usually, within levels of an index)
\item \link{dupKeys} give a logical index to duplicated rows of a keyed data frame, AND the rows of which they are duplicates
\item \link{enth} alias for ordinal
\item \link{episcript} run a script in an environment that defines the the passed arguments
\item \link{f} alias for as.flag
\item \link{falseAmt} generic
\item \link{falseAmt.nm} AMT defined where EVID is not 1
\item \link{falseDv} generic
\item \link{falseDv.nm} DV is defined where EVID is not 0
\item \link{filename} generate standard file name (internal)
\item \link{first} generic
\item \link{first.logical} repeat for each element the position of the first TRUE element (usually, within levels of an index)
\item \link{fixedwidth} convert to fixed-width format
\item \link{fixedwidth} convert a data.frame to fixed-width format
\item \link{forbak} impute NAs using last observation carried forward and then next observation carried backward
\item \link{format.comment} format comment 
\item \link{format.flag} format flag
\item \link{format.miDate} format miDate
\item \link{format.miDateTime} format miDateTime
\item \link{format.miTime} format miTime
\item \link{getCovs} return non-commented non-duplicated rows of a NONMEM data set (internal)
\item \link{getCwres} return the conditional weighted residuals pertinent to a given run (internal, expects cwtab1.deriv)
\item \link{getPars} return the non-duplicated (ID) rows corresponding to the specified filename (internal)
\item \link{getTabs} return the observation rows (EVID==0) corresponding to the specified filename (internal)
\item \link{getdname} extract the path and file from the DATA block in the control stream associated with filename (internal)
\item \link{groupnames} construct a single vector of group names from possibly multiple indicies to the plotting data set (internal)
\item \link{hash} prepend a character to each line of output
\item \link{hide} generic
\item \link{hide.data.frame} comment out the specified rows of a data frame, appending a flag that suggests the reason
\item \link{ibw} calculate ideal body weight
\item \link{ind.cwres} compute conditional weighted residuals (internal)
\item \link{is.cwres.readable.file} compute conditional weighted residuals (internal)
\item \link{ke} calculate elimination constant
\item \link{key} return the key of a keyed data frame
\item \link{key<-} assign a key
\item \link{lbm} calculate lean body mass
\item \link{left.keyed} produce left join of two keyed data frames
\item \link{locf} impute NA using last observation carried forward
\item \link{maxChar} return the number of printed characters for the widest element of x
\item \link{merge.keyed} merge keyed data frames, preserving attributes
\item \link{merge.nm} merge nm objects
\item \link{metaSub} generic
\item \link{metaSub.character} systematically substitute elements in a character vector
\item \link{metaSub.filename} systematically substitute elements in a text file
\item \link{minus.keyed} drop rows in x that have matching rows in y
\item \link{minus.moot} drop moot rows
\item \link{moot} generic
\item \link{moot.nm} identify moot rows (rows not influencing NONMEM estimates)
\item \link{myriwish} support \code{\link{SimulateOmega}} (internal)
\item \link{naInContext} display rows of data with missing values, as well as other rows with the same key
\item \link{naKeys} detect rows for which one or more key fields is NA
\item \link{nix} identify Unix-like platforms (internal)
\item \link{nm} give a zero-row data frame with suitable columns and column classes; i.e. a template for NMTRAN data sets
\item \link{nm.pl} prepare commandlines for nm.pl
\item \link{nmPlots} a list of functions that plot nm objects
\item \link{noPk} generic
\item \link{noPk.nm} rows where EVID is never 0 within SUBJ
\item \link{nocb} impute NA with next observation carried backward
\item \link{ordinal} generic
\item \link{ordinal.logical} repeat for each element the position of the n-th TRUE element (usually, within levels of an index)
\item \link{packageCheck} load a package and run package-level examples
\item \link{panel.covplot} plot distributions with respect to reference values; i.e. combine panel.cuts, panel.densitystrip, and panel.ref
\item \link{panel.cuts} for each strip, plot percent observations in each vertical category defined by cuts
\item \link{panel.densitystrip} for each strip, plot a filled polygon representing smoothed density of the distribution
\item \link{panel.ref} plot a reference region in a stripplot
\item \link{plot.nm} generate standard plots for an nm object using \code{\link{nmPlots}}
\item \link{plus.keyed} produce and outer join of keyed data frames
\item \link{plus.rigged} merge an nm object with a rigged data frame
\item \link{predoseDv} generic
\item \link{predoseDv.nm} DV is defined before the first record within SUBJ where EVID is 1
\item \link{prev} calculate the previous element for each element of x
\item \link{print.comment} print comment
\item \link{print.flag} print flag
\item \link{print.keyed.summary} print keyed summary
\item \link{print.miTemporal} print miTemporal
\item \link{print.nm.summary} print nm summary
\item \link{purge.dir} purge a directory (internal)
\item \link{purge.files} purge files (internal)
\item \link{qsub} prepare commandlines for qsub
\item \link{read.cwres.data} compute conditional weighted residuals (internal)
\item \link{read.nm} read a csv file and try to transform to nm
\item \link{reapply} apply a function across cells of an indexed vector, giving an identically-indexed result
\item \link{rep.comment} repeat comment
\item \link{rep.flag} repeat flag
\item \link{rep.miTemporal} repeat miTemporal
\item \link{resample} generic
\item \link{resample.csv.filename} create replicate data sets by stratified sampling with replacement, after reading csv file
\item \link{resample.data.frame} create replicate data sets by stratified sampling with replacement
\item \link{resample.filename} create replicate data sets by stratified sampling with replacement, after reading file
\item \link{rig} generic
\item \link{rig.nm} generate extra rows, spaced across each subject's timecourse, for obtaining model predictions in NONMEM (EVID==2)
\item \link{rinvchisq} generate inverse chi-square distribution
\item \link{rinvgamma} generate inverse gamma distribution given n, df, and sigma estimate
\item \link{riwish} generate inverse Wishart distribution
\item \link{rlog} generate a combined run log for multiple NONMEM runs
\item \link{runCommand} issue the system call that invokes NONMEM (internal)
\item \link{runNonmem} process a request for NONMEM invocation
\item \link{runhead} determine whether each element is the start of a run
\item \link{safe.call} call a function, passing only those extra arguments that the function accepts
\item \link{seq.miTemporal} generate miTemporal sequence
\item \link{setCwres} append conditional weighted residuals to an appropriate file
\item \link{sort.keyed} sort a keyed data frame
\item \link{sorted} check whether a x is sorted on the specified columns
\item \link{sqrtm} support \code{compute.cwres}
\item \link{stableMerge}produce a left join, with strict error checking
\item \link{star} replace asterisk in x with y (internal)
\item \link{strain} reduce x to those elements that occur in options (internal)
\item \link{summary.keyed} summarize a keyed data frame
\item \link{summary.nm} summarize an nm object
\item \link{synthesis} sequentially left-join an arbitrary number of data frames, picking up novel columns (internal)
\item \link{text2decimal} convert mixed text to decimal
\item \link{tmax} calculate the time of the maximum concentration
\item \link{transform.keyed} transform a keyed data frame, preserving class
\item \link{unconditional} generic
\item \link{unconditional.data.frame} return an all-TRUE logical vector of length nrow(x)
\item \link{unconditional.default} return an all-TRUE logical vector of length nrow(x)
\item \link{uniKey} generic
\item \link{uniKey.keyed} create a single character vector from all the key columns
\item \link{nmVersion} extract NONMEM version specification from configuration file
\item \link{where} generic
\item \link{where.logical} return a logical vector identifying the n-th TRUE element in x (usually, within levels of an index)
\item \link{win} identify Windows platforms (internal)
\item \link{write.nm} write an nm object to file
\item \link{xtfrm.comment} produce a numeric vector that sorts in the same order as comment
\item \link{xtfrm.flag} produce a numeric vector that sorts in the same order as flag
\item \link{xtfrm.miTemporal} produce a numeric vector that sorts in the same order as miTemporal
\item \link{zeroAmt} generic
\item \link{zeroAmt.nm} AMT is zero where EVID is 1
\item \link{zeroDv} generic
\item \link{zeroDv.nm} DV is zero where EVID is zero
} 
} 

